[pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

Author: pre-commit-ci[bot]

tests/conftest.py

@@ -260,8 +260,8 @@ def gt_tm_annotation() -> np.ndarray:
     for i in range(10):
         tm[i][i] = 1
     for i in range(10, 15):
-        tm[i-5][i] = 1
-    for j in range(2,5):
-        for i in range(2,5):
+        tm[i - 5][i] = 1
+    for j in range(2, 5):
+        for i in range(2, 5):
             tm[i][j] = 0.3 if i != j else 0.4
     return tm

tests/problems/cross_modality/test_mixins.py

@@ -109,7 +109,7 @@ def test_cell_transition_pipeline(
 
     @pytest.mark.fast()
     @pytest.mark.parametrize("forward", [True, False])
-    @pytest.mark.parametrize("mapping_mode",["max", "sum"])
+    @pytest.mark.parametrize("mapping_mode", ["max", "sum"])
     @pytest.mark.parametrize("problem_kind", ["cross_modality"])
     def test_annotation_mapping(
         self, adata_anno: Tuple[AnnData, AnnData], forward: bool, mapping_mode, gt_tm_annotation
@@ -122,14 +122,14 @@ def test_annotation_mapping(
         tp[problem_keys].set_solution(MockSolverOutput(gt_tm_annotation), overwrite=True)
         annotation_label = "celltype1" if forward else "celltype2"
         result = tp.annotation_mapping(
-            mapping_mode=mapping_mode,
-            annotation_label=annotation_label,
-            forward=forward,
-            source="src",
-            target="tgt"
+            mapping_mode=mapping_mode, annotation_label=annotation_label, forward=forward, source="src", target="tgt"
         )
         if forward:
-            expected_result = adata_src.uns["expected_max1"] if mapping_mode == "max" else adata_src.uns["expected_sum1"]
+            expected_result = (
+                adata_src.uns["expected_max1"] if mapping_mode == "max" else adata_src.uns["expected_sum1"]
+            )
         else:
-            expected_result = adata_tgt.uns["expected_max2"] if mapping_mode == "max" else adata_tgt.uns["expected_sum2"]
+            expected_result = (
+                adata_tgt.uns["expected_max2"] if mapping_mode == "max" else adata_tgt.uns["expected_sum2"]
+            )
         assert (result[annotation_label] == expected_result).all()

tests/problems/space/test_mixins.py

@@ -112,11 +112,16 @@ def test_annotation_mapping(self, adata_anno: AnnData, forward: bool, mapping_mo
             forward=forward,
         )
         if forward:
-            expected_result = adata_anno.uns["expected_max1"] if mapping_mode == "max" else adata_anno.uns["expected_sum1"]
+            expected_result = (
+                adata_anno.uns["expected_max1"] if mapping_mode == "max" else adata_anno.uns["expected_sum1"]
+            )
         else:
-            expected_result = adata_anno.uns["expected_max2"] if mapping_mode == "max" else adata_anno.uns["expected_sum2"]
+            expected_result = (
+                adata_anno.uns["expected_max2"] if mapping_mode == "max" else adata_anno.uns["expected_sum2"]
+            )
         assert (result[annotation_label] == expected_result).all()
 
+
 class TestSpatialMappingAnalysisMixin:
     @pytest.mark.parametrize("sc_attr", [{"attr": "X"}, {"attr": "obsm", "key": "X_pca"}])
     @pytest.mark.parametrize("var_names", ["0", [str(i) for i in range(20)]])

tests/problems/time/test_mixins.py

@@ -51,7 +51,7 @@ def test_cell_transition_full_pipeline(self, gt_temporal_adata: AnnData, forward
         np.testing.assert_allclose(present_cell_type_marginal, 1.0)
 
     @pytest.mark.fast()
-    @pytest.mark.parametrize("forward",[True, False])
+    @pytest.mark.parametrize("forward", [True, False])
     @pytest.mark.parametrize("mapping_mode", ["max", "sum"])
     @pytest.mark.parametrize("problem_kind", ["temporal"])
     def test_annotation_mapping(self, adata_anno: AnnData, forward: bool, mapping_mode, gt_tm_annotation):
@@ -63,11 +63,15 @@ def test_annotation_mapping(self, adata_anno: AnnData, forward: bool, mapping_mo
         annotation_label = "celltype1" if forward else "celltype2"
         result = problem.annotation_mapping(
             mapping_mode=mapping_mode, annotation_label=annotation_label, forward=forward, source=0, target=1
-            )
+        )
         if forward:
-            expected_result = adata_anno.uns["expected_max1"] if mapping_mode == "max" else adata_anno.uns["expected_sum1"]
+            expected_result = (
+                adata_anno.uns["expected_max1"] if mapping_mode == "max" else adata_anno.uns["expected_sum1"]
+            )
         else:
-            expected_result = adata_anno.uns["expected_max2"] if mapping_mode == "max" else adata_anno.uns["expected_sum2"]
+            expected_result = (
+                adata_anno.uns["expected_max2"] if mapping_mode == "max" else adata_anno.uns["expected_sum2"]
+            )
         assert (result[annotation_label] == expected_result).all()
 
     @pytest.mark.fast()